Starting phenix.real_space_refine on Fri Mar 22 07:55:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/03_2024/6p18_20233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/03_2024/6p18_20233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/03_2024/6p18_20233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/03_2024/6p18_20233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/03_2024/6p18_20233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/03_2024/6p18_20233.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 123 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20120 2.51 5 N 5793 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 950": "OE1" <-> "OE2" Residue "C GLU 987": "OE1" <-> "OE2" Residue "C GLU 1020": "OE1" <-> "OE2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C GLU 1342": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D GLU 765": "OE1" <-> "OE2" Residue "D PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1052": "OE1" <-> "OE2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F GLU 369": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32673 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1153 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "2" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1142 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10568 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2665 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 6, 'TRANS': 318} Chain breaks: 2 Chain: "P" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1165 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "Q" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1261 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 244 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16874 SG CYS D 70 58.979 119.013 85.312 1.00 46.06 S ATOM 16888 SG CYS D 72 60.321 122.141 84.051 1.00 47.41 S ATOM 16996 SG CYS D 85 58.195 120.359 81.163 1.00 51.55 S ATOM 17020 SG CYS D 88 61.752 119.701 81.629 1.00 46.73 S ATOM 22708 SG CYS D 814 58.114 52.188 74.105 1.00 40.48 S ATOM 23273 SG CYS D 888 60.903 55.573 74.913 1.00 31.50 S ATOM 23324 SG CYS D 895 58.341 53.893 77.348 1.00 27.28 S ATOM 23345 SG CYS D 898 60.983 51.584 76.680 1.00 26.31 S Time building chain proxies: 16.55, per 1000 atoms: 0.51 Number of scatterers: 32673 At special positions: 0 Unit cell: (158.834, 179.088, 172.692, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 143 16.00 P 123 15.00 Mg 1 11.99 O 6491 8.00 N 5793 7.00 C 20120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.39 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 12 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 47 sheets defined 43.7% alpha, 13.1% beta 50 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 10.95 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.531A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.222A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.657A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.044A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.884A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.799A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.192A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.887A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.737A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.552A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.629A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.812A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.065A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 removed outlier: 4.095A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.777A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.921A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.694A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.606A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.907A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.522A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.573A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.596A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.763A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.991A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.325A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.941A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.798A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.343A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1361 through 1375 removed outlier: 4.515A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 114 through 135 removed outlier: 3.690A pdb=" N ASP F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 216 through 232 Processing helix chain 'F' and resid 243 through 257 removed outlier: 3.673A pdb=" N LYS F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 294 removed outlier: 4.195A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.681A pdb=" N LEU F 330 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.576A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.528A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.642A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 4.309A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 444 removed outlier: 4.644A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 467 Processing helix chain 'P' and resid 9 through 29 removed outlier: 3.801A pdb=" N SER P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 44 Processing helix chain 'P' and resid 59 through 74 removed outlier: 3.779A pdb=" N GLY P 63 " --> pdb=" O ASN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 89 Processing helix chain 'P' and resid 93 through 103 removed outlier: 3.500A pdb=" N ILE P 97 " --> pdb=" O SER P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 150 Proline residue: P 143 - end of helix Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 38 through 48 Processing helix chain 'Q' and resid 60 through 74 Processing helix chain 'Q' and resid 77 through 89 Processing helix chain 'Q' and resid 93 through 104 Processing helix chain 'Q' and resid 122 through 151 removed outlier: 3.536A pdb=" N CYS Q 126 " --> pdb=" O SER Q 122 " (cutoff:3.500A) Proline residue: Q 143 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 6.812A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.518A pdb=" N GLU A 60 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.560A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 16 removed outlier: 4.013A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 105 removed outlier: 6.286A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.509A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.186A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.440A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.891A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 98 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.151A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.640A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AC1, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.966A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.089A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.526A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.526A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.783A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.962A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1065 through 1066 removed outlier: 7.099A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.677A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 877 " --> pdb=" O GLY C 926 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.850A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.548A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.623A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.689A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.228A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.942A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.513A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.645A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.503A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 984 " --> pdb=" O GLU D 993 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 966 removed outlier: 4.040A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.962A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.571A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AE9, first strand: chain 'D' and resid 1164 through 1165 Processing sheet with id=AF1, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 4.008A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 108 through 109 1363 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 16.11 Time building geometry restraints manager: 14.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8109 1.33 - 1.45: 6360 1.45 - 1.57: 18478 1.57 - 1.69: 244 1.69 - 1.81: 249 Bond restraints: 33440 Sorted by residual: bond pdb=" N LEU F 305 " pdb=" CA LEU F 305 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.27e-02 6.20e+03 6.68e+00 bond pdb=" N GLU D1276 " pdb=" CA GLU D1276 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.16e-02 7.43e+03 6.67e+00 bond pdb=" N LEU D1275 " pdb=" CA LEU D1275 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.08e-02 8.57e+03 6.03e+00 bond pdb=" N LYS C 991 " pdb=" CA LYS C 991 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.33e-02 5.65e+03 5.75e+00 bond pdb=" N LEU C 992 " pdb=" CA LEU C 992 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.69e-02 3.50e+03 4.80e+00 ... (remaining 33435 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.85: 1263 105.85 - 112.92: 17743 112.92 - 120.00: 11980 120.00 - 127.07: 14169 127.07 - 134.15: 521 Bond angle restraints: 45676 Sorted by residual: angle pdb=" C GLY B 209 " pdb=" N THR B 210 " pdb=" CA THR B 210 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C MET F 322 " pdb=" N ASN F 323 " pdb=" CA ASN F 323 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.80e+01 angle pdb=" N LYS C 991 " pdb=" CA LYS C 991 " pdb=" C LYS C 991 " ideal model delta sigma weight residual 113.28 107.33 5.95 1.22e+00 6.72e-01 2.38e+01 angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 angle pdb=" CA GLU Q 11 " pdb=" CB GLU Q 11 " pdb=" CG GLU Q 11 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 ... (remaining 45671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17345 17.93 - 35.86: 2096 35.86 - 53.78: 634 53.78 - 71.71: 177 71.71 - 89.64: 30 Dihedral angle restraints: 20282 sinusoidal: 9265 harmonic: 11017 Sorted by residual: dihedral pdb=" CA LEU C 397 " pdb=" C LEU C 397 " pdb=" N SER C 398 " pdb=" CA SER C 398 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP D 710 " pdb=" C ASP D 710 " pdb=" N GLY D 711 " pdb=" CA GLY D 711 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA SER C 398 " pdb=" C SER C 398 " pdb=" N ALA C 399 " pdb=" CA ALA C 399 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 20279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4493 0.073 - 0.145: 622 0.145 - 0.218: 53 0.218 - 0.291: 2 0.291 - 0.364: 5 Chirality restraints: 5175 Sorted by residual: chirality pdb=" CB ILE D 707 " pdb=" CA ILE D 707 " pdb=" CG1 ILE D 707 " pdb=" CG2 ILE D 707 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL D1280 " pdb=" CA VAL D1280 " pdb=" CG1 VAL D1280 " pdb=" CG2 VAL D1280 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 5172 not shown) Planarity restraints: 5519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 324 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO F 325 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 325 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 325 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO C 190 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO C 520 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.039 5.00e-02 4.00e+02 ... (remaining 5516 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 564 2.67 - 3.23: 27476 3.23 - 3.78: 51384 3.78 - 4.34: 67563 4.34 - 4.90: 109894 Nonbonded interactions: 256881 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.110 2.170 nonbonded pdb=" O3' A R 11 " pdb="MG MG D1503 " model vdw 2.116 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.144 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.191 2.170 nonbonded pdb=" OE2 GLU D 981 " pdb=" OG SER D 994 " model vdw 2.302 2.440 ... (remaining 256876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = (chain 'P' and resid 7 through 150) selection = (chain 'Q' and resid 7 through 150) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.250 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 97.380 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33440 Z= 0.218 Angle : 0.754 10.854 45676 Z= 0.427 Chirality : 0.050 0.364 5175 Planarity : 0.006 0.080 5519 Dihedral : 17.451 89.640 13188 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.10), residues: 3802 helix: -2.17 (0.09), residues: 1574 sheet: -2.23 (0.23), residues: 399 loop : -2.89 (0.11), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 326 HIS 0.005 0.001 HIS D 104 PHE 0.028 0.002 PHE F 266 TYR 0.021 0.001 TYR D 679 ARG 0.007 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 582 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7947 (ttpp) REVERT: A 117 HIS cc_start: 0.7606 (p-80) cc_final: 0.7341 (p-80) REVERT: B 229 GLU cc_start: 0.7479 (tp30) cc_final: 0.7140 (tp30) REVERT: C 524 ILE cc_start: 0.8837 (tt) cc_final: 0.8593 (tt) REVERT: C 696 ASP cc_start: 0.7953 (t70) cc_final: 0.7635 (t70) REVERT: C 952 GLN cc_start: 0.8164 (mt0) cc_final: 0.7928 (mt0) REVERT: D 140 TYR cc_start: 0.7162 (m-10) cc_final: 0.6832 (m-80) REVERT: D 802 ASP cc_start: 0.7850 (m-30) cc_final: 0.7609 (m-30) REVERT: D 984 LEU cc_start: 0.8002 (tt) cc_final: 0.7770 (tt) REVERT: D 1146 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6932 (tm-30) REVERT: D 1243 LEU cc_start: 0.8188 (tp) cc_final: 0.7977 (tp) REVERT: F 276 MET cc_start: 0.7472 (ppp) cc_final: 0.7185 (ppp) REVERT: P 87 TYR cc_start: 0.8795 (t80) cc_final: 0.8287 (t80) REVERT: Q 21 GLU cc_start: 0.7842 (tp30) cc_final: 0.7623 (mm-30) REVERT: Q 90 HIS cc_start: 0.8294 (t70) cc_final: 0.8066 (t-170) outliers start: 9 outliers final: 1 residues processed: 588 average time/residue: 0.5006 time to fit residues: 446.3699 Evaluate side-chains 396 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 150 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 199 optimal weight: 0.0980 chunk 157 optimal weight: 10.0000 chunk 305 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 354 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 37 HIS B 128 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 447 HIS C 622 ASN C 673 HIS C1008 GLN C1313 HIS D 196 GLN D 232 ASN D 300 GLN D 450 HIS D 477 GLN D 504 GLN D 777 HIS D 875 ASN D1049 GLN D1098 GLN D1108 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN D1252 HIS D1259 GLN F 128 ASN F 258 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN P 90 HIS Q 12 GLN ** Q 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33440 Z= 0.184 Angle : 0.547 8.846 45676 Z= 0.291 Chirality : 0.041 0.157 5175 Planarity : 0.004 0.059 5519 Dihedral : 16.080 88.582 5633 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.59 % Allowed : 12.81 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 3802 helix: -0.09 (0.12), residues: 1597 sheet: -2.07 (0.24), residues: 389 loop : -2.36 (0.12), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 326 HIS 0.004 0.001 HIS D 430 PHE 0.025 0.001 PHE F 306 TYR 0.022 0.001 TYR C 70 ARG 0.009 0.000 ARG P 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 430 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7420 (ptt180) REVERT: B 145 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8340 (ttpp) REVERT: C 239 MET cc_start: 0.7762 (tmm) cc_final: 0.7467 (tmm) REVERT: C 397 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6581 (mp) REVERT: C 524 ILE cc_start: 0.8782 (tt) cc_final: 0.8495 (tt) REVERT: C 696 ASP cc_start: 0.8119 (t70) cc_final: 0.7895 (t70) REVERT: C 1108 ASN cc_start: 0.8448 (p0) cc_final: 0.8123 (p0) REVERT: D 96 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8129 (ptpt) REVERT: D 140 TYR cc_start: 0.7152 (m-10) cc_final: 0.6784 (m-80) REVERT: D 233 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8112 (mtmm) REVERT: D 526 VAL cc_start: 0.8944 (m) cc_final: 0.8720 (m) REVERT: D 571 ASP cc_start: 0.7143 (t70) cc_final: 0.6936 (t0) REVERT: D 1208 ASP cc_start: 0.6173 (t0) cc_final: 0.5947 (t0) REVERT: F 276 MET cc_start: 0.7492 (ppp) cc_final: 0.7275 (ppp) REVERT: P 12 GLN cc_start: 0.5525 (tp40) cc_final: 0.3070 (tp40) REVERT: Q 21 GLU cc_start: 0.8071 (tp30) cc_final: 0.7654 (tm-30) REVERT: Q 90 HIS cc_start: 0.8350 (t70) cc_final: 0.8077 (t-170) outliers start: 52 outliers final: 30 residues processed: 461 average time/residue: 0.4767 time to fit residues: 342.9357 Evaluate side-chains 412 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 379 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 294 optimal weight: 0.0970 chunk 241 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 354 optimal weight: 4.9990 chunk 383 optimal weight: 5.9990 chunk 315 optimal weight: 0.6980 chunk 351 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 214 ASN D 157 GLN D 196 GLN D 294 ASN D 910 ASN D 962 ASN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN P 68 GLN Q 12 GLN Q 151 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 33440 Z= 0.358 Angle : 0.610 10.557 45676 Z= 0.319 Chirality : 0.043 0.158 5175 Planarity : 0.004 0.053 5519 Dihedral : 16.113 88.515 5633 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.45 % Allowed : 15.38 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3802 helix: 0.52 (0.13), residues: 1595 sheet: -1.91 (0.25), residues: 391 loop : -2.14 (0.13), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 15 HIS 0.007 0.001 HIS D 430 PHE 0.018 0.002 PHE F 302 TYR 0.033 0.002 TYR F 148 ARG 0.010 0.000 ARG P 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 402 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 TYR cc_start: 0.6974 (m-80) cc_final: 0.6654 (m-80) REVERT: C 130 MET cc_start: 0.8798 (ttm) cc_final: 0.8577 (ttm) REVERT: C 239 MET cc_start: 0.7871 (tmm) cc_final: 0.7540 (tmm) REVERT: C 516 ASP cc_start: 0.7116 (t0) cc_final: 0.6826 (t70) REVERT: C 696 ASP cc_start: 0.8206 (t70) cc_final: 0.7981 (t70) REVERT: C 800 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7832 (mtm) REVERT: C 922 ASN cc_start: 0.8094 (m-40) cc_final: 0.7690 (m110) REVERT: D 96 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8189 (ptpt) REVERT: D 140 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: D 233 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8123 (mtmm) REVERT: D 571 ASP cc_start: 0.7143 (t70) cc_final: 0.6937 (t0) REVERT: D 697 MET cc_start: 0.8707 (ttp) cc_final: 0.8163 (ttp) REVERT: D 1215 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6326 (pt0) REVERT: E 55 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6541 (tp30) REVERT: F 144 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7403 (pp) REVERT: F 276 MET cc_start: 0.7579 (ppp) cc_final: 0.6488 (ppp) REVERT: F 362 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7844 (t0) REVERT: F 403 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7604 (t0) REVERT: P 12 GLN cc_start: 0.5344 (tp-100) cc_final: 0.2260 (tp40) REVERT: P 15 TRP cc_start: 0.7428 (t60) cc_final: 0.6994 (t60) REVERT: P 101 TYR cc_start: 0.8508 (t80) cc_final: 0.8266 (t80) REVERT: P 132 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7578 (tm-30) REVERT: Q 21 GLU cc_start: 0.8153 (tp30) cc_final: 0.7755 (tm-30) outliers start: 80 outliers final: 48 residues processed: 454 average time/residue: 0.4520 time to fit residues: 325.6219 Evaluate side-chains 432 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 376 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 356 optimal weight: 10.0000 chunk 376 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 337 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 219 GLN D 196 GLN D 341 ASN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN P 68 GLN P 135 ASN Q 90 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33440 Z= 0.347 Angle : 0.598 9.569 45676 Z= 0.312 Chirality : 0.043 0.162 5175 Planarity : 0.004 0.052 5519 Dihedral : 16.114 89.108 5633 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.12 % Allowed : 16.97 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3802 helix: 0.75 (0.13), residues: 1600 sheet: -1.81 (0.25), residues: 394 loop : -1.97 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 997 HIS 0.006 0.001 HIS D 430 PHE 0.023 0.001 PHE F 302 TYR 0.042 0.002 TYR F 137 ARG 0.009 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 393 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 TYR cc_start: 0.7096 (m-80) cc_final: 0.6841 (m-80) REVERT: C 516 ASP cc_start: 0.7073 (t0) cc_final: 0.6803 (t0) REVERT: C 696 ASP cc_start: 0.8211 (t70) cc_final: 0.8002 (t70) REVERT: C 800 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7886 (mtm) REVERT: C 826 ASP cc_start: 0.7424 (m-30) cc_final: 0.7201 (t0) REVERT: C 922 ASN cc_start: 0.8085 (m-40) cc_final: 0.7736 (m-40) REVERT: D 96 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8250 (ptpt) REVERT: D 724 MET cc_start: 0.8005 (ttm) cc_final: 0.7791 (mtm) REVERT: D 1208 ASP cc_start: 0.6284 (t0) cc_final: 0.6018 (t0) REVERT: E 55 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6615 (tp30) REVERT: F 362 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7853 (t0) REVERT: F 403 ASP cc_start: 0.7889 (m-30) cc_final: 0.7589 (t0) REVERT: P 12 GLN cc_start: 0.5000 (tp-100) cc_final: 0.2800 (tp40) REVERT: P 15 TRP cc_start: 0.7377 (t60) cc_final: 0.6988 (t60) REVERT: P 101 TYR cc_start: 0.8536 (t80) cc_final: 0.8259 (t80) REVERT: P 132 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7610 (tm-30) REVERT: P 140 MET cc_start: 0.7207 (tmm) cc_final: 0.7000 (tmm) REVERT: Q 21 GLU cc_start: 0.8178 (tp30) cc_final: 0.7777 (tm-30) outliers start: 102 outliers final: 65 residues processed: 458 average time/residue: 0.4496 time to fit residues: 329.9786 Evaluate side-chains 428 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 359 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 321 optimal weight: 0.8980 chunk 260 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 338 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 147 GLN B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 341 ASN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN Q 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33440 Z= 0.315 Angle : 0.587 10.113 45676 Z= 0.305 Chirality : 0.042 0.199 5175 Planarity : 0.004 0.050 5519 Dihedral : 16.094 89.372 5633 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.09 % Allowed : 18.56 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3802 helix: 0.89 (0.13), residues: 1602 sheet: -1.72 (0.24), residues: 413 loop : -1.83 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D1193 HIS 0.006 0.001 HIS D 430 PHE 0.023 0.001 PHE F 221 TYR 0.027 0.002 TYR F 421 ARG 0.010 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 385 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 TYR cc_start: 0.7103 (m-80) cc_final: 0.6843 (m-80) REVERT: C 516 ASP cc_start: 0.7114 (t0) cc_final: 0.6856 (t0) REVERT: C 696 ASP cc_start: 0.8222 (t70) cc_final: 0.8002 (t70) REVERT: C 800 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7862 (mtm) REVERT: C 922 ASN cc_start: 0.8077 (m-40) cc_final: 0.7707 (m-40) REVERT: D 52 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6823 (mm-30) REVERT: D 96 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8242 (ptpt) REVERT: D 140 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: D 221 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8908 (mm) REVERT: D 1040 MET cc_start: 0.4755 (ppp) cc_final: 0.2751 (ptt) REVERT: E 55 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: F 362 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7852 (t0) REVERT: F 403 ASP cc_start: 0.7855 (m-30) cc_final: 0.7559 (t0) REVERT: P 12 GLN cc_start: 0.4711 (tp-100) cc_final: 0.2639 (tp40) REVERT: P 101 TYR cc_start: 0.8570 (t80) cc_final: 0.8277 (t80) REVERT: P 132 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7606 (tm-30) REVERT: Q 21 GLU cc_start: 0.8170 (tp30) cc_final: 0.7783 (tm-30) outliers start: 101 outliers final: 79 residues processed: 463 average time/residue: 0.4471 time to fit residues: 331.3346 Evaluate side-chains 448 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 363 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 4.9990 chunk 339 optimal weight: 40.0000 chunk 74 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 377 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 341 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33440 Z= 0.252 Angle : 0.569 11.615 45676 Z= 0.297 Chirality : 0.041 0.207 5175 Planarity : 0.004 0.050 5519 Dihedral : 16.027 89.572 5633 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.27 % Allowed : 19.23 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 3802 helix: 1.05 (0.13), residues: 1597 sheet: -1.58 (0.25), residues: 408 loop : -1.71 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D1193 HIS 0.008 0.001 HIS F 455 PHE 0.041 0.001 PHE F 221 TYR 0.032 0.001 TYR F 137 ARG 0.010 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 379 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8736 (mmtm) REVERT: C 516 ASP cc_start: 0.7177 (t0) cc_final: 0.6909 (t0) REVERT: C 922 ASN cc_start: 0.8087 (m-40) cc_final: 0.7727 (m-40) REVERT: D 96 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8222 (ptpt) REVERT: D 140 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: D 1040 MET cc_start: 0.4563 (ppp) cc_final: 0.3009 (ptt) REVERT: E 55 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6666 (tp30) REVERT: F 362 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7849 (t0) REVERT: P 101 TYR cc_start: 0.8509 (t80) cc_final: 0.8188 (t80) REVERT: P 132 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7585 (tm-30) REVERT: Q 21 GLU cc_start: 0.8155 (tp30) cc_final: 0.7786 (tm-30) outliers start: 107 outliers final: 84 residues processed: 460 average time/residue: 0.4572 time to fit residues: 336.6951 Evaluate side-chains 451 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 363 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 210 optimal weight: 0.1980 chunk 375 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 235 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 341 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33440 Z= 0.205 Angle : 0.548 11.648 45676 Z= 0.287 Chirality : 0.041 0.159 5175 Planarity : 0.004 0.051 5519 Dihedral : 15.930 89.564 5633 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.87 % Allowed : 19.93 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3802 helix: 1.23 (0.13), residues: 1599 sheet: -1.41 (0.25), residues: 405 loop : -1.63 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D1193 HIS 0.004 0.001 HIS D 430 PHE 0.035 0.001 PHE F 221 TYR 0.047 0.001 TYR P 142 ARG 0.012 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 386 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 TYR cc_start: 0.7100 (m-80) cc_final: 0.6845 (m-80) REVERT: C 429 MET cc_start: 0.7924 (mmm) cc_final: 0.7625 (mtt) REVERT: C 516 ASP cc_start: 0.7138 (t0) cc_final: 0.6845 (t0) REVERT: C 826 ASP cc_start: 0.7429 (m-30) cc_final: 0.7180 (t0) REVERT: C 922 ASN cc_start: 0.8111 (m-40) cc_final: 0.7764 (m-40) REVERT: D 96 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8219 (ptpt) REVERT: D 140 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: D 1040 MET cc_start: 0.4504 (ppp) cc_final: 0.3197 (ptt) REVERT: D 1189 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7538 (tpp) REVERT: D 1208 ASP cc_start: 0.6416 (t0) cc_final: 0.5982 (t0) REVERT: E 55 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6690 (tp30) REVERT: F 362 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7877 (t0) REVERT: F 456 MET cc_start: 0.8296 (tpp) cc_final: 0.7894 (mpp) REVERT: P 64 MET cc_start: 0.7502 (tpp) cc_final: 0.7205 (tpp) REVERT: P 132 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7582 (tm-30) REVERT: Q 21 GLU cc_start: 0.8133 (tp30) cc_final: 0.7783 (tm-30) REVERT: Q 65 LEU cc_start: 0.9055 (tt) cc_final: 0.8819 (tp) outliers start: 94 outliers final: 76 residues processed: 455 average time/residue: 0.4507 time to fit residues: 328.6789 Evaluate side-chains 454 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 373 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 295 optimal weight: 30.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 147 GLN B 208 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 490 GLN D 196 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33440 Z= 0.167 Angle : 0.538 12.073 45676 Z= 0.281 Chirality : 0.040 0.170 5175 Planarity : 0.003 0.049 5519 Dihedral : 15.814 89.491 5633 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.60 % Allowed : 20.54 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3802 helix: 1.41 (0.13), residues: 1600 sheet: -1.18 (0.26), residues: 384 loop : -1.52 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D1193 HIS 0.003 0.001 HIS A 23 PHE 0.033 0.001 PHE F 221 TYR 0.029 0.001 TYR P 142 ARG 0.013 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 391 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.8758 (m-80) cc_final: 0.8557 (m-80) REVERT: C 46 GLN cc_start: 0.7312 (mm-40) cc_final: 0.6643 (mm-40) REVERT: C 397 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6500 (mp) REVERT: C 516 ASP cc_start: 0.7141 (t0) cc_final: 0.6923 (t0) REVERT: C 725 GLN cc_start: 0.8352 (tt0) cc_final: 0.8151 (tt0) REVERT: C 922 ASN cc_start: 0.8075 (m-40) cc_final: 0.7693 (m-40) REVERT: D 96 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8180 (ptpt) REVERT: D 140 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: D 1040 MET cc_start: 0.4341 (ppp) cc_final: 0.3294 (ptt) REVERT: D 1189 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7511 (tpp) REVERT: D 1208 ASP cc_start: 0.6415 (t0) cc_final: 0.6056 (t0) REVERT: E 55 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.5933 (tp30) REVERT: F 362 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7878 (t0) REVERT: F 456 MET cc_start: 0.8209 (tpp) cc_final: 0.7909 (mpp) REVERT: P 64 MET cc_start: 0.7408 (tpp) cc_final: 0.7166 (tpp) REVERT: P 132 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7560 (tm-30) REVERT: Q 21 GLU cc_start: 0.8070 (tp30) cc_final: 0.7664 (tm-30) REVERT: Q 65 LEU cc_start: 0.9028 (tt) cc_final: 0.8765 (tp) REVERT: Q 139 PHE cc_start: 0.8489 (t80) cc_final: 0.8271 (t80) outliers start: 85 outliers final: 67 residues processed: 446 average time/residue: 0.4402 time to fit residues: 313.6913 Evaluate side-chains 438 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 365 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 chunk 328 optimal weight: 0.5980 chunk 350 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 331 optimal weight: 0.9980 chunk 349 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 686 GLN C1008 GLN D 196 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33440 Z= 0.346 Angle : 0.606 13.397 45676 Z= 0.314 Chirality : 0.043 0.186 5175 Planarity : 0.004 0.058 5519 Dihedral : 15.925 88.935 5633 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.57 % Allowed : 21.00 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3802 helix: 1.18 (0.13), residues: 1605 sheet: -1.27 (0.26), residues: 391 loop : -1.50 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP P 15 HIS 0.005 0.001 HIS D 430 PHE 0.035 0.001 PHE F 221 TYR 0.038 0.002 TYR F 137 ARG 0.015 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 370 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.8800 (m-80) cc_final: 0.8532 (m-80) REVERT: C 696 ASP cc_start: 0.8250 (t70) cc_final: 0.7965 (t70) REVERT: C 800 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7858 (mtm) REVERT: C 826 ASP cc_start: 0.7460 (m-30) cc_final: 0.7215 (t0) REVERT: C 922 ASN cc_start: 0.8057 (m-40) cc_final: 0.7697 (m-40) REVERT: D 96 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8256 (ptpt) REVERT: D 140 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: D 1040 MET cc_start: 0.4329 (ppp) cc_final: 0.3350 (ptt) REVERT: D 1189 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7503 (tpp) REVERT: E 55 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.5966 (tp30) REVERT: F 362 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7902 (t0) REVERT: F 456 MET cc_start: 0.8331 (tpp) cc_final: 0.8021 (mpp) REVERT: P 64 MET cc_start: 0.7430 (tpp) cc_final: 0.7135 (tpp) REVERT: P 132 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7603 (tm-30) REVERT: Q 21 GLU cc_start: 0.8185 (tp30) cc_final: 0.7810 (tm-30) REVERT: Q 65 LEU cc_start: 0.9084 (tt) cc_final: 0.8832 (tp) outliers start: 84 outliers final: 74 residues processed: 431 average time/residue: 0.4415 time to fit residues: 305.2140 Evaluate side-chains 442 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 362 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 0.9980 chunk 370 optimal weight: 6.9990 chunk 226 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 357 optimal weight: 4.9990 chunk 309 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 147 GLN C 120 GLN C 193 ASN D 196 GLN D 341 ASN D 489 ASN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33440 Z= 0.185 Angle : 0.561 14.286 45676 Z= 0.292 Chirality : 0.041 0.161 5175 Planarity : 0.003 0.057 5519 Dihedral : 15.831 89.576 5633 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.60 % Allowed : 21.22 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3802 helix: 1.37 (0.13), residues: 1600 sheet: -1.08 (0.26), residues: 381 loop : -1.43 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP P 15 HIS 0.004 0.001 HIS Q 102 PHE 0.035 0.001 PHE F 221 TYR 0.040 0.001 TYR F 137 ARG 0.014 0.000 ARG D1345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 373 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 524 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 922 ASN cc_start: 0.8059 (m-40) cc_final: 0.7698 (m-40) REVERT: D 96 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8222 (ptpt) REVERT: D 489 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7902 (p0) REVERT: D 1040 MET cc_start: 0.4315 (ppp) cc_final: 0.3530 (ptt) REVERT: D 1189 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7510 (tpp) REVERT: D 1208 ASP cc_start: 0.6306 (t0) cc_final: 0.5846 (t0) REVERT: E 55 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.5920 (tp30) REVERT: F 362 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7919 (t0) REVERT: F 456 MET cc_start: 0.8268 (tpp) cc_final: 0.8056 (mpp) REVERT: P 132 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7561 (tm-30) REVERT: Q 21 GLU cc_start: 0.8115 (tp30) cc_final: 0.7778 (tm-30) REVERT: Q 65 LEU cc_start: 0.9040 (tt) cc_final: 0.8784 (tp) outliers start: 85 outliers final: 73 residues processed: 436 average time/residue: 0.4550 time to fit residues: 319.4472 Evaluate side-chains 442 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 363 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 0.8980 chunk 329 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 285 optimal weight: 0.0470 chunk 45 optimal weight: 10.0000 chunk 85 optimal weight: 0.0030 chunk 309 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 193 ASN D 196 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.180689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153197 restraints weight = 41132.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153049 restraints weight = 108860.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151873 restraints weight = 46981.213| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33440 Z= 0.146 Angle : 0.555 13.980 45676 Z= 0.288 Chirality : 0.040 0.159 5175 Planarity : 0.003 0.059 5519 Dihedral : 15.728 89.965 5633 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.14 % Allowed : 21.61 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3802 helix: 1.54 (0.13), residues: 1600 sheet: -0.96 (0.26), residues: 402 loop : -1.34 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 15 HIS 0.003 0.000 HIS A 23 PHE 0.035 0.001 PHE F 221 TYR 0.041 0.001 TYR F 137 ARG 0.014 0.000 ARG D1345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6691.99 seconds wall clock time: 121 minutes 30.23 seconds (7290.23 seconds total)